Sequence analysis of proteins separated by polyacrylamide gel electrophoresis: towards an integrated protein database

Quantitative study of lipase secretion, extracellular lipolysis, and lipid storage in the yeast Yarrowia lipolytica grown in the presence of olive oil: analogies with lipolysis in humans

Lipase secretion, extracellular lipolysis, and fatty acid uptake were quantified in the yeast Yarrowia lipolytica grown in the presence of olive oil and/or glucose. Specific lipase assays, Western blot analysis, and ELISA indicated that most of the lipase activity measured in Y. lipolytica cultures resulted from the YLLIP2 lipase. Lipase production was triggered by olive oil and, during the first hours of culture, most of the lipase activity and YLLIP2 immunodetection remained associated with the yeast cells. YLLIP2 was then released in the culture medium before it was totally degraded by proteases. Olive oil triglycerides were largely degraded when the lipase was still attached to the cell wall. The fate of lipolysis products in the culture medium and inside the yeast cell, as well as lipid storage, was investigated simultaneously by quantitative TLC-FID and GC analysis. The intracellular levels of free fatty acids (FFA) and triglycerides increased transiently and were dependent on the carbon sources. A maximum fat storage of 37.8% w/w of yeast dry mass was observed with olive oil alone. A transient accumulation of saturated FFA was observed whereas intracellular triglycerides became enriched in unsaturated fatty acids. So far, yeasts have been mainly used for studying the intracellular synthesis, storage, and mobilization of neutral lipids. The present study shows that yeasts are also interesting models for studying extracellular lipolysis and fat uptake by the cell. The quantitative data obtained here allow for the first time to establish interesting analogies with gastrointestinal and vascular lipolysis in humans.

A pilot study of proteomic profiles of human hepatocellular carcinoma in the United States

Human hepatocellular carcinoma (HCC) is one of the commonest causes of mortality among solid organ malignancies. The incidence of HCC in the United States is rising. Few proteomic biomarker studies have been done in U.S. populations. Tumor and nonmalignant tissue from three American patients with hepatitis and non-hepatitis-associated HCC were analyzed to find common differences in protein expression. Proteins were separated by 2D electrophoresis (isoelectric focusing followed by 10% SDS-PAGE). Gels were fixed and then stained with Coomassie brilliant blue. Digitization and processing were performed using the PDQuest software. The Student's t-test was used to detect quantitative protein changes between tumor and nonmalignant liver consistent in all sample pairs with a cutoff made at P < 0.01. This yielded a total of 20 spots with significant (>2 fold) abundance changes. Matrix-assisted laser desorption ionization mass spectrometry analysis was performed using Waters Micomass M@LDI SYSTEM. The proteins were then identified using manual ProFound. Among the 20 spots, 10 showed overexpression and 10 showed underexpression in tumor. Overexpressed proteins included beta-5-tubulin, beta-actin, vimentin, hypermethylated in cancer 2 protein, heat-shock 70-kDa protein 9B, serum albumin, 39S ribosomal protein L45, butyrophilin, autoimmune regulator, and transcription factor ETV7. Underexpressed proteins included BiP protein, superoxide dismutase, peroxiredoxin 2, inoraganic pyrophosphatase, keratin 8, carbonic anhydrase 1, repulsive guidance molecule, catalase, C-1-tetrahydrofolate synthase, and hemoglobin alpha-2. Of particular interest, the protein autoimmune regulator was expressed 14-fold higher in tumor tissue, suggesting it may have a role in HCC. Validation and further investigation of these protein changes may lead to the discovery of new molecular targets for therapy, biomarkers for early detection, and new endpoints for therapeutic efficacy and toxicity.

Improved Method for Proteome Mapping of the Liver by 2-DE MALDI-TOF MS

Identifying the liver proteome has been the subject of intensified research. Notably, due to their strong heterogeneity in size, charge, solubility, and relative abundance, different strategies of pre-fractionation must be employed to increase the number of identifiable proteins. In our efforts, we used two different lysis buffers in sequence, a liquid-phase IEF pre-fractionation and separation of protein mixtures at three different pH ranges (3-10, 5-8, and 7-10). Then, >15 000 gel digested proteins were investigated. We report an identification of 590 different gene products, including some isoforms. More than 150 proteins have not been reported so far by two-dimensional electrophoresis (2-DE) proteome mapping. We further studied the transcript expression of more than 33 000 genes in rat liver to explore correlations between transcript and protein expression. Overall, we report a method for the separation of rat liver proteins and their identification by mass spectrometry. The newly identified proteins will enable an improved understanding of liver biology.

Proteomic analyses using an accurate mass and time tag strategy

An accurate mass and time (AMT) tag approach for proteomic analyses has been developed over the past several years to facilitate comprehensive high-throughput proteomic measurements. An AMT tag database for an organism, tissue, or cell line is established by initially performing standard shotgun proteomic analysis and, most importantly, by validating peptide identifications using the mass measurement accuracy of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) and liquid chromatography (LC) elution time constraint. Creation of an AMT tag database largely obviates the need for subsequent MS/MS analyses, and thus facilitates high-throughput analyses. The strength of this technology resides in the ability to achieve highly efficient and reproducible one-dimensional reversed-phased LC separations in conjunction with highly accurate mass measurements using FTICR MS. Recent improvements allow for the analysis of as little as picrogram amounts of proteome samples by minimizing sample handling and maximizing peptide recovery. The nanoproteomics platform has also demonstrated the ability to detect >10(6) differences in protein abundances and identify more abundant proteins from subpicogram amounts of samples. The AMT tag approach is poised to become a new standard technique for the in-depth and high-throughput analysis of complex organisms and clinical samples, with the potential to extend the analysis to a single mammalian cell.

Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate–polyacrylamide gels and polyvinyldifluoride membranes

The resolving power of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) combined with isoelectric focusing in two-dimensional gel electrophoresis has made it one of the most important techniques for resolving complex mixtures, and it is of great importance for proteome mapping projects. As a result of this, methods for postelectrophoretic protein characterization are of great interest as exemplified by in situ protease digestion combined with mass spectrometry (MS), which is the method of choice for identification of proteins. In this study we have developed and compared methods for recovering intact proteins from polyacrylamide gels and electroblotting membranes to define efficient methods compatible with MS. These methods complement in situ digestion protocols and allow determination of the molecular mass of whole proteins separated by SDS-PAGE. Passive elution of proteins from SDS-PAGE gels was efficient only in the presence of SDS, whereas electroelution was achieved using buffers without SDS. Surface-enhanced laser desorption/ionization MS (SELDI-MS) analysis of proteins eluted in the presence of SDS was possible using ion exchange ProteinChip arrays for concentration of sample and removal of SDS. Comparison of different electroblotting methods verified that the different membranes and buffers were equally efficient for transfer of proteins in the range 20-100 kDa. Elution from polyvinyldifluoride membranes was most efficient using either concentrated solutions of trifluoroacetic acid (TFA) or combinations of 8M urea and 1% Triton X-100, 1% Tween 20, or 40% isopropanol. The same result was obtained using nitrocellulose membranes, except that these were incompatible with organic solvent and TFA. Elution by TFA was compatible with matrix-assisted laser desorption/ionization MS (MALDI-MS) but was complicated by a high degree of trifluoroacetylation of the proteins. Alternatively, elution by 8M urea+1% Triton X-100, 1% Tween 20, or 40% isopropanol was compatible with both SELDI-MS and MALDI-MS. Eluted proteins were identified in MS experiments by intact mass determination, by peptide mapping, and by MS/MS analysis.

"Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping

We describe here a new approach for the identification of affinity-bound proteins by proteolytic generation and mass spectrometric analysis of their antibody bound epitope peptides (epitope excision). The cardiac muscle protein troponin T was chosen as a protein antigen because of its diagnostic importance in myocardial infarct, and its previously characterised epitope structure. Two monoclonal antibodies (IgG1-1B10 and IgG1-11.7) raised against intact human troponin T were found to be completely cross reactive with bovine heart troponin T. A combination of immuno-affinity isolation, partial proteolytic degradation (epitope excision), mass spectrometric peptide mapping, and database analysis was used for the direct identification of Tn T from bovine heart cell lysate. Selective binding of the protein was achieved by addition of bovine heart cell lysate to the Sepharose-immobilised monoclonal antibodies, followed by removal of supernatant material containing unbound protein. While still bound to the affinity matrix the protein was partially degraded thereby generating a set of affinity-bound, overlapping peptide fragments comprising the epitope. Following dissociation from the antibody the epitope peptides were analysed by matrix assisted laser desorption-ionisation (MALDI) and electrospray-ionisation (ESI) mass spectrometry. The peptide masses identified by mass spectrometry were used to perform an automated database search, combined with a search for a common "epitope motif". This procedure resulted in the unequivocal identification of the protein from biological material with only a minimum number of peptide masses, and requiring only limited mass-determination accuracy. The dramatic increase of selectivity for identification of the protein by combining the antigen-antibody specificity with the redundancy of peptide sequences renders this "affinity-proteomics" approach a powerful tool for mass spectrometric identification of proteins from biological material.

Assessment of protein expression by means of 2-D gel electrophoresis with and without mass spectrometry

Careful examination of current literature, particularly over the last 5 years, reveals a wide range of approaches for the relative quantification of protein expression in cells, tissues, and body fluids. In view of such an observation, it is reasonable to ask whether researchers need new methods, or whether it is more productive to optimize and tune already existing ones. It is generally agreed that none of the existing methodologies on its own can give a full account of protein expression in a complex medium; this limitation, however, has not prevented the use of existing methods to provide valuable information on a wide range of proteins, where their expression has been correlated to certain pathologies and/or to pharmacological, genetic, or environmental factors. In the present work, an attempt is made to review the application of one of these methodologies, namely two-dimensional polyacrylamide gel electrophoresis on its own or in conjunction with mass spectrometry, to assess protein expression, particularly when such expression can be correlated to certain pathologies.

Enrichment of serum amyloid proteins by hydrophobic interaction chromatography combined with two-dimensional electrophoresis with immobilised pH gradients

Serum amyloid A protein was subjected to one-step octyl-Sepharose extraction in three different dimensions. Elution was performed partly without UV recording, and with urea or guanidine-based buffers. The eluent was applied directly to denaturing two-dimensional electrophoresis with immobilised pH gradient, or octyl-Sepharose extracted fractions were pooled and lyophilised before application. Proteins were characterised by N-terminal analysis or mass spectrometry. In most of the species that were studied, previously undescribed serum amyloid proteins were detected. Compared to conventional strategies, the presented techniques are more rational and yield more comprehensive information. The presented data also provide a basis for novel perspectives regarding certain inflammatory conditions.

The proteome: anno Domini 2002

We present some current definitions related to functional and structural proteomics and the human proteome, and we review the following aspects of proteome analysis: Classical 2-D map analysis (isoelectric focusing (IEF) followed by SDS-PAGE); Quantitative proteomics (isotope-coded affinity tag (ICAT), fluorescent stains) and their use in e.g., tumor analysis and identification of new target proteins for drug development; Electrophoretic pre-fractionation (how to see the hidden proteome!); Multidimensional separations, such as: (a) coupled size-exclusion and reverse-phase (RP)-HPLC; (b) coupled ion-exchange and RP-HPLC; (c) coupled RP-HPLC and RP-HPLC at 25/60 degrees C; (d) coupled RP-HPLC and capillary electrophoresis (CE); (e) metal affinity chromatography coupled with CE; Protein chips. Some general conclusions are drawn on proteome analysis and we end this review by trying to decode the glass ball of the aruspex and answer the question: "Quo vadis, proteome"?

Proteomic map and database of lymphoblastoid proteins

Advances in genomics have led to the accumulation of an unprecedented amount of data, giving rise to a new field in biochemistry, proteomics. We used a combination of two dimensional gel electrophoresis, analysis and annotation using third-generation software, and mass spectrometry to establish the proteome maps of lymphoblastoid B-cells, a prerequisite for analysis of drug effects and lymphocyte cell diseases. About 1200 protein spots were detected and characterised in terms of their isoelectric point, molecular mass and expression. The present status of proteomic technologies, as well as a description of the usefulness of human hematopoietic cells proteomic database are discussed.

Proteome analysis of bacterial pathogens

Combining two-dimensional electrophoresis with mass spectrometry resulted in a powerful technology ideally suited to recognize and identify proteins of pathogenic microorganisms. This classical proteome analysis is now complemented by capillary chromatography/mass spectrometry combinations, miniaturization by chip technology and protein interaction investigations. Comparative proteomics is used to reveal vaccine candidates and pathogenicity factors. Immunoproteomics identifies specific and nonspecific antigens. For the management of the huge data amounts, bioinformatics is a valuable instrument for the construction of complex protein databases.

Predominant Identification of RNA-binding Proteins in Fas-induced Apoptosis by Proteome Analysis

Proteome analysis of Jurkat T cells was performed in order to identify proteins that are modified during apoptosis. Subtractive analysis of two-dimensional gel patterns of apoptotic and nonapoptotic cells revealed differences in 45 protein spots. 37 protein spots of 21 different proteins were identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization mass spectrometry. The hnRNPs A0, A2/B1, A3, K, and R; the splicing factors p54(nrb), SRp30c, ASF-2, and KH-type splicing regulatory protein (FUSE-binding protein 2); and alpha NAC, NS1-associated protein 1, and poly(A)-binding protein 4 were hitherto unknown to be involved in apoptosis. The putative cleavage sites of the majority of the proteins could be calculated by the molecular masses and isoelectric points in the two-dimensional electrophoresis gel, the peptide mass fingerprints, and after translation by treatment with recombinant caspase-3. Remarkably, 15 of the 21 identified proteins contained the RNP or KH motif, the best characterized RNA-binding motifs.

Identification of post-translationally modified proteins in proteome studies

Proteome studies are powerful tools to solve many different problems in metabolism, signal transduction, drug discovery, and other areas of interest in life sciences. Up to now, high-sensitive methods for protein identification after two-dimensional gel electrophoresis using mass spectrometry are available. However, the identification of post-translational modifications after two-dimensional gel electrophoresis is still an unsolved problem. In this paper, we want to give several examples for the successful identification of post-translational modifications and point mutations.

Identification of HL60 Proteins Affected by 5-Aminolevulinic Acid-Based Photodynamic Therapy Using Mass Spectrometric Approach

A combination of mass spectrometric techniques was used for identification of HL60 leukemia cell proteins affected by 5-aminolevulinic acid-based photodynamic therapy (ALA-PDT). We compared two-dimensional electrophoresis (2-DE) protein maps of ALA-treated non-irradiated and irradiated cells and found extensive changes in the proteome of HL60 cells. The silver-stained 2-DE pattern of HL60 proteins contained more than 1 350 spots. Matrix-assisted laser desorption/ionisation mass spectrometry and microcapillary liquid chromatography/tandem mass spectrometry have identified twelve proteins differing in their intensity or position following ALA-PDT. Several endoplasmic reticulum, mitochondrial, ribosomal and cytoplasmic proteins were determined showing the impact of ALA-PDT-mediated cytotoxicity on some cellular pathways.

A two dimensional electrophoresis database of a human Jurkat T-cell line

About 2000 protein spots of human Jurkat T-cells were detected by high resolution two-dimensional gel electrophoresis (2-DE) and were characterized in terms of their isoelectric point and molecular mass. A 2-DE database was constructed and is available at http://www.mpiib-berlin.mpg.de/2D-PAGE/. At present the database contains 67 identified protein spots. These proteins were identified after tryptic digestion by peptide mass fingerprinting with delayed extraction-matrix assisted laser desorption/ionization-mass spectrometry (DE-MALDI-MS). Proteins with a sequence coverage of at least 30% were introduced in the database. This sequence coverage could not always be obtained by using only the matrix alpha-cyano-4-hydroxycinnamic acid (CHCA) for the mass analysis. Therefore, an additional mass spectrum was recorded by using 2,5-dihydroxybenzoic acid (DHB). Usually, additional mass peaks were detected and together with the mass spectrum of CHCA this resulted in the desired sequence coverage.

Mass spectrometry: a tool for the identification of proteins separated by gels

Mass spectrometry (MS) has become the technique of choice to identify proteins. This has been largely accomplished by the combination of high-resolution two-dimensional (2-D) gel separation with robotic sample preparation, automated MS measurement, data analysis, and database query. Developments during the last five years in MS associated with protein gel separation are reviewed.

Comparative proteome analysis of Helicobacter pylori

Helicobacter pylori, the causative agent of gastritis, ulcer and stomach carcinoma, infects approximately half of the worlds population. After sequencing the complete genome of two strains, 26695 and J99, we have approached the demanding task of investigating the functional part of the genetic information containing macromolecules, the proteome. The proteins of three strains of H. pylori, 26695 and J99, and a prominent strain used in animal models SS1, were separated by a high-resolution two-dimensional electrophoresis technique with a resolution power of 5000 protein spots. Up to 1800 protein species were separated from H. pylori which had been cultivated for 5 days on agar plates. Using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) peptide mass fingerprinting we have identified 152 proteins, including nine known virulence factors and 28 antigens. The three strains investigated had only a few protein spots in common. We observe that proteins with an amino acid exchange resulting in a net change of only one charge are shifted in the two-dimensional electrophoresis (2-DE) pattern. The expression of 27 predicted conserved hypothetical open reading frames (ORFs) and six unknown ORFs were confirmed. The growth conditions of the bacteria were shown to have an effect on the presence of certain proteins. A preliminary immunoblotting study using human sera revealed that this approach is ideal for identifying proteins of diagnostic or therapeutic value. H. pylori 2-DE patterns with their identified protein species were added to the dynamic 2D-PAGE database (http://www.mpiib-berlin.mpg.de/2D-PAGE/). This basic knowledge of the proteome in the public domain will be an effective instrument for the identification of new virulence or pathogenic factors, and antigens of potentially diagnostic or curative value against H. pylori.

Modified expression of plasma glutathione peroxidase and manganese superoxide dismutase in human renal cell carcinoma

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) is a powerful tool to separate thousands of polypeptides and to highlight the modification of protein expression in malignant diseases. By applying 2-D PAGE to ten normal human kidney and ten homologous renal cell carcinoma (RCC) tissues, we found two peptides in all ten normal tissues but not in RCCs and, conversely, two peptides were detected in all RCCs but not in normal tissues. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and internal sequence analysis, the two first peptides were identified as two isoforms of plasma glutathione peroxidase (GPxP). The two other peptides isolated in all RCCs but not in normal tissues were identified by N-terminal sequence analysis as multimeric forms of manganese superoxide dismutase (Mn-SOD). No multimeric Mn-SODs and only two monomeric forms were detected in normal tissues. GPxP and Mn-SOD are metallo-enzymes encoded on chromosome 5q32 and on chromosome 6p25, respectively. Their regions are within the locus 5q21-->qter and 6q21-6q27 on which deletions and translocations are described in some cytogenetic studies of RCC transformation. Therefore, our results might suggest a correlation between the modified expression of GPxP and Mn-SOD in tumor tissues and chromosomal modifications, and that the two proteins may be putative markers for diagnosis of RCC.

Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens

In 1993, the WHO declared tuberculosis a global emergency on the basis that there are 8 million new cases per year. The complete genome of the strain H37Rv of the causative microorganism, Mycobacterium tuberculosis, comprising 3924 genes has been sequenced. We compared the proteomes of two non-virulent vaccine strains of M. bovis BCG (Chicago and Copenhagen) with two virulent strains of M. tuberculosis (H37Rv and Erdman) to identify protein candidates of value for the development of vaccines, diagnostics and therapeutics. The mycobacterial strains were analysed by two-dimensional electrophoresis (2-DE) combining non-equilibrium pH gradient electrophoresis (NEPHGE) with SDS-PAGE. Distinct and characteristic proteins were identified by mass spectrometry and introduced into a dynamic 2-DE database (http://www.mpiib-berlin.mpg.de/2D-PAGE). Silver-stained 2-DE patterns of mycobacterial cell proteins or culture supernatants contained 1800 or 800 spots, respectively, from which 263 were identified. Of these, 54 belong to the culture supernatant. Sixteen and 25 proteins differing in intensity or position between M. tuberculosis H37Rv and Erdman, and H37Rv and M. bovis BCG Chicago, respectively, were identified and categorized into protein classes. It is to be hoped that the availability of the mycobacterial proteome will facilitate the design of novel measures for prevention and therapy of one of the great health threats, tuberculosis.

Preparative high-resolution two-dimensional electrophoresis enables the identification of RNA polymerase B transcription factor 3 as an apoptosis-associated protein in the human BL60-2 Burkitt lymphoma cell line

Apoptosis or programmed cell death is essential in the process of controlling lymphocyte growth and selection. We identified RNA polymerase B transcription factor 3 (BTF3), which is associated with anti-IgM antibody-mediated apoptosis, using a subclone of the human Burkitt lymphoma cell line BL60. To identify the transcription factor BTF3, which is expressed only in minor amounts, we used preparative high-resolution two-dimensional gel electrophoresis (2DE) employing carrier ampholytes for isoelectric focusing. Comparison of the 2DE protein patterns from apoptotic and nonapoptotic cells showed BTF3 as a predominantly altered protein spot. The characterization of the differentially expressed transcription factor and 13 marker proteins described in this study were performed by internal Edman microsequencing and/or by peptide mass fingerprinting using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The proteome analysis was significantly improved by performing the newly developed preparative high-resolution two-dimensional gels employing high protein concentrations.

Study of Burkitt lymphoma cell line proteins by high resolution two-dimensional gel electrophoresis and nanoelectrospray mass spectrometry

We paper describe a mass spectrometric approach generally applicable for the rapid identification and characterization of proteins isolated by two-dimensional gel electrophoresis (2-DE). The highly sensitive nanoflow-electrospray mass spectrometry employing a quadrupole-time of flight mass spectrometer was used for the direct identification of proteins from the peptide mixture generated from only one high resolution 2-DE gel without high performance liquid chromatography (HPLC) separation or Edman sequencing. Due to the high sensitivity and high mass accuracy of the instrument employed, this technique proved to be a powerful tool for the identification of proteins from femtomole amounts of materials. We applied the technique for the investigation of Burkitt lymphoma BL60 cell proteins. This cell line has been used as a model to assign apoptosis-associated proteins by subtractive analysis of normal and apoptotic cells. From the nuclear fraction of these cells, 36 protein spots were examined, from only one micropreparative Coomassie Brilliant Blue R-250 stained gel, after proteolytic digestion by matrix assisted laser desorption ionization (MALDI) and nanospray mass spectrometry (MS). In combination with database searches, of 33 proteins were successfully identified by nanospray-MS/MS-sequencing of up to eight peptides per protein. Three proteins were new proteins not listed in any of the available databases. Some of the identified proteins are known to be involved in apoptosis processes, the others were common proteins in the eukaryotic cell. The given technique and the protein data are the basis for construction of a database to compare normal and apoptosis-induced cells and, further, to enable fast screening of drug impact in apoptosis-associated processes.

Identification of apoptosis-associated proteins in a human Burkitt lymphoma cell line. Cleavage of heterogeneous nuclear ribonucleoprotein A1 by caspase 3

Apoptosis or programmed cell death is essential in the process of controlling lymphocyte growth and selection. We identified proteins that are involved in anti-IgM antibody-mediated apoptosis using a subclone of the human Burkitt lymphoma cell line BL60. Apoptosis-associated proteins were detected by high resolution two-dimensional gel electrophoresis on a micropreparative scale. Comparison of the high resolution two-dimensional gel electrophoresis protein patterns from apoptotic and non-apoptotic cells showed differences in approximately 80 spots including protein modifications. Analysis of the predominantly altered proteins was performed by internal Edman microsequencing and/or by peptide mass fingerprinting using matrix-assisted laser desorption/ionization mass spectrometry. Analysis was significantly improved by using new micropreparative high resolution two-dimensional gels employing high protein concentrations. The following 12 apoptosis-associated proteins were identified: heterogeneous nuclear ribonucleoprotein (hnRNP) A1, hnRNP C1/C2, FUSE-binding protein, dUTPase, lymphocyte-specific protein LSP1, UV excision repair protein RAD23 homologue B (HHR23B), 60 S acidic ribosomal protein P0 (L10E), heterochromatin protein 1 homologue alpha (HP1alpha), nucleolin, lamin, neutral calponin, and actin. Fragmentation of actin, hnRNP A1, hnRNP C1/C2, 60 S acidic ribosomal protein P0, lamin, and nucleolin could be inhibited by benzyloxycarbonyl-Asp(OMe)-Glu(OMe)-Val-Asp(OMe)-fluoromethyl ketone, a selective irreversible inhibitor of CPP32 (caspase 3).

Application of two-dimensional protein gels in biotechnology

The optimal use of biological systems for technologically developed products will not be achieved until biological systems are completely defined in biochemical terms. Two-dimensional polyacrylamide gel electrophoresis, 2-D gels, are contributing to this goal. These gels separate complex mixtures of proteins into individual polypeptide species. The ultimate use of 2-D gels is the construction of cellular 2-D gel databases which identify the proteins on the gels and catalog their responses to different environmental conditions. In addition to these global analyses, many applications for 2-D gels in basic, applied and clinical research have been shown.

The Australian Proteome Analysis Facility (APAF): assembling large scale proteomics through integration and automation

The field of proteomics opens new possibilities for the mass screening of proteins from many different sources. While genomics is well understood to be a big science field, proteomics is just emerging as such. This paper describes the setting up of the first national proteomics facility. The facility has been funded by the Australian government and this funding has allowed the design of purpose built, integrated laboratories with state of the art equipment for large scale proteome research.

Occupational applications of a human cancer research model

Many bladder cancers are indolent, and since there are no biomarkers to predict progression, the prognosis is problematic. Utilizing an in vitro/in vivo human uroepithelial cell (SV-HUC.PC) transformation system, we investigated several molecular events occurring along the continuum of exposure to disease outcome as potential biomarkers for occupational carcinogenesis. The model also served to generate information on the occupational carcinogenicity of N-hydroxy-4,4'-methylene bis(2-chloroaniline) [N-OH-MOCA]. Two of 14 groups of SV-HUC.PC treated with various concentrations of N-OH-MOCA formed carcinomas in athymic nude mice. Each of the biomarkers investigated demonstrated potential for interventions/prevention applications of occupational bladder cancers but will require validation and further evaluation. Those investigated displaying potential occupational utility included the induction of ornithine decarboxylase (ODC), DNA adducts, and altered proteins, as detected on HUC two-dimensional polyacrylamide gel electrophoresis protein maps.

Identification and characterization of heat shock protein 27 protein species in human myocardial two-dimensional electrophoresis patterns

Immunostaining of heat shock protein 27 (Hsp27) protein species on two-dimensional electrophoresis (2-DE) gels with enhanced sensitivity yields 59 spots reacting with anti-Hsp27 antibodies. Recombinant Hsp27 exists in 2-DE as two major protein species which comigrate in the human myocardial pattern with Hsp27 spots C754 and D899 as defined in the heart high-performance 2-DE database (http://www.mdc-berlin.de/emu/heart/). Preparative electrophoresis of human myocardial proteins and analysis of the enriched mass range 20-30 kDa by 2-DE revealed eight protein spots (C438, C582, C658, C697, C754, C595, C750) from the human myocardial database and a new spot not previously detected on silver-stained gels. These spots were identified as Hsp27 protein species by enzymatic in-gel-digestion and analysis by matrix assisted laser desorption-ionization (MALDI) peptide mass fingerprinting and, in part, MALDI-post source decay sequencing of single fragments. Possible post-translational modifications were investigated: immunostaining tests with anti-phospho-serine/-threonine/-tyrosine antibodies, although positive for other myocardial proteins, were negative for presumed Hsp27 protein species; likewise, periodate-glycostaining assays and biotinylation screening did not detect modifications in the investigated Hsp27 protein species.

Primary structures of proteins characterized by proteinase K digestion and matrix-assisted laser desorption/ionization mass spectrometry

To improve the sequence ions of a protein in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), proteinase K was used to digest the protein followed by MALDI-MS characterization of the peptide fragments. The primary structures of three proteins, insulin B chain, cytochrome c and lysozyme, were determined by this method. A series of peptide fragments including those differentiated by one residue can be produced from the protein by using proteinase K digestion, thus providing support to the protein sequence. The peptide fragments liberated from proteinase K proteolysis of the insulin B chain allow the protein to be partially sequenced. Furthermore, some of the residues are double or triple checked by generating a variety of fragments. The same method was used to investigate cytochrome c and lysozyme denaturated in 3 M guanidine hydrochloride. The success of the method relies on the intrinsic properties of proteinase K and accurate determination of the peptide fragments by MALDI-MS.

Visualization of prosomes (MCP-proteasomes), intermediate filament and actin networks by "instantaneous fixation" preserving the cytoskeleton

A new "instantaneous" fixation/extraction procedure, yielding good preservation of intermediate filaments (IFs) and actin filaments when applied at 37 degrees C, has been explored to reexamine the relationships of the prosomes to the cytoskeleton. Prosomes are protein complexes of variable subunit composition, including occasionally a small RNA, which were originally observed as trans-acting factors in untranslated mRNPs. Constituting also the proteolytic core of the 26S proteasomes, they are also called "multicatalytic proteinase (MCP) complexes" or "20S-Proteasomes." In Triton X-100-extracted epithelial, fibroblastic, and muscle cells, prosome particles were found associated primarily with the IFs (Olink-Coux et al., 1994). Application of "instantaneous fixation" has now led to the new observation that a major fraction of prosome particles, composed of specific sets of subunits, is distributed in variable proportions between the IFs and the microfilament/ stress fiber system in PtK1 epithelial cells and human fibroblasts. Electron microscopy using gold-labeled antibodies confirms this dual localization on classical whole mounts and on cells exposed to instantaneous fixation. In contrast to the resistance of the prosome-IF association, a variable fraction of the prosome particles is released from the actin cytoskeleton by Triton X-100 when applied prior to fixation. Moreover, in vitro copolymerization of prosomes with G-actin made it possible to observe "ladder-like" filamentous structures in the electron microscope, in which the prosome particles, like the "rungs of a ladder," laterally crosslink two or more actin filaments in a regular pattern. These results demonstrate that prosomes are bound in the cell not only to IFs but also to the actin cytoskeleton and, furthermore, not only within large M(r) complexes (possibly mRNPs and/or 26S proteasomes), but also directly, as individual prosome particles.

High-performance human myocardial two-dimensional electrophoresis database: edition 1996

The master gel of the human myocardial two-dimensional electrophoresis (2-DE) gel database contains about 3300 protein spots characterized in terms of isoelectric point (pI) and molecular mass. A high-performance technique was applied, using large gels (23 x 30 cm). Isoelectric focusing with anodic sample preparation and nonequilibrium running conditions (NEPHGE) was combined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in 15% acrylamide gels in the second dimension. The range of pI extends from pH 4.5 to 9.6. Seventy proteins were identified by combinations of amino acid analysis, N-terminal and internal sequencing, immunostaining, matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS) peptide mass fingerprinting, post-source decay MALDI-MS and ladder sequencing by carboxypeptidase P. The identification of additional proteins, not found in the master gel, was achieved by immunoblotting. Unequivocal identification with high sensitivity and good yield was obtained by combining internal sequencing and MALDI-MS. In-gel digestion, the concentration and purification of peptides in a peptide collecting device, and the improved FRAGMOD program for peptide mass fingerprinting have added to the security and sensitivity of identification. The high-performance human myocardial 2-DE database was built up with proteins detected by the TOPSPOT program. Spots within six sections of the whole pattern are clickable. Protein description includes detailed information about identification, characterization, and links to the related SWISS-PROT, other 2-DE databases and Medline entries. The database is constructed in accordance with four of the rules for a federated database.

Identification of human myocardial proteins separated by two-dimensional electrophoresis using an effective sample preparation for mass spectrometry

Peptide mass fingerprinting is a powerful tool for the identification of proteins separated by two-dimensional gel electrophoresis (2-DE). The identification of in-gel digested proteins by peptide mass fingerprinting was significantly improve in comparison to blot-digests by using a peptide-collecting device. This device allows the effective purification and concentration of enzymatic digests of low-intensity spots without expensive equipment and is described in detail. Sensitivity in the fmol range was demonstrated by unequivocal identification of bovine serum albumin after sodium dodecyl sulfate--polyacrylamide gel electrophoresis. Furthermore the high performance liquid chromatography pattern of in-gel digests indicated a 2- to 3-fold higher yield of the separated peptides. Therefore, a higher amount of the peptides was available to perform N-terminal sequencing. The identification of 16 proteins from a high-resolution 2-DE gel map of human myocardium tissue has been achieved by means of this technique. Three of these proteins were associated with changes in spot intensity with dilated cardiomyopathy.

Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome

The two-dimensional electrophoresis (2-DE) technique developed by Klose in 1975 (Humangenetik 1975, 26, 211-234), independently of the technique developed by O'Farrell (J. Biol. Chem. 1975, 250, 4007-4021), has been revised in our laboratory and an updated protocol is presented. This protocol is the result of our experience in using this method since its introduction. Many modifications and suggestions found in the literature were also tested and then integrated into our original method if advantageous. Gel and buffer composition, size of gels, use of stacking gels or not, necessity of isoelectric focusing (IEF) gel incubation, freezing of IEF gels or immediate use, carrier ampholytes versus Immobilines, regulation of electric current, conditions for staining and drying the gels - these and other problems were the subject of our concern. Among the technical details and special equipment which constitute our 2-DE method presented here, a few features are of particular significance: (i) sample loading onto the acid side of the IEF gel with the result that both acidic and basic proteins are well resolved in the same gel; (ii) use of large (46 x 30 cm) gels to achieve high resolution, but without the need of unusually large, flat gel equipment; (iii) preparation of ready-made gel solutions which can be stored frozen, a prerequisite, among others, for high reproducibility. Using the 2-DE method described we demonstrate that protein patterns revealing more than 10 000 polypeptide spots can be obtained from mouse tissues. This is by far the highest resolution so far reported in the literature for 2-DE of complex protein mixtures. The 2-DE patterns were of high quality with regard to spot shape and background. The reproducibility of the protein patterns is demonstrated and shown to be thoroughly satisfactory. An example is given to show how effectively 2-DE of high resolution and reproducibility can be used to study the genetic variability of proteins in an interspecific mouse backcross (Mus musculus x Mus spretus) established by the European Backcross Collaborative Group for mapping the mouse genome. We outline our opinion that the structural analysis of the human genome, currently pursued most intensively on a worldwide scale, should be accompanied by a functional analysis of the genome that starts from the proteins of the organism.

Chamber-specific expression of human myocardial proteins detected by two-dimensional gel electrophoresis

High resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by computer-assisted image analysis (PDQUEST) was used to screen atrial and ventricular protein patterns for quantitative and qualitative differences in protein expression. Myocardial proteins from left ventricular (LV) and right atrial (RA) samples from end-stage, failing explanted hearts and from a healthy donor heart (control) were separated by 2-D large gel electrophoresis. Ten RA versus ten LV gels from explanted dilated cardiomyopathic (DCM) hearts were analyzed for quantitative differences in their spot patterns. Of the 197 spots matched to every gel, 40 spots differed significantly in intensity between RA and LV for DCM patients. A larger number of atrial and ventricular gels (20 RA, 20 LV) from DCM patients and from a healthy donor heart (4 RA, 4 LV gels) were analyzed for qualitative differences in protein expression. Three protein spots (SSP 1120: M(r)/pI:20.5 kDa/4.6; SSP 1119: M(r)/pI:20.6 kDa/4.5; SSP 0117:M(r)/pI:20.7/ < 4.5) that are present in all RA gels for DCM patients are absent in all LV gels. Two protein spots (SSP 0112: M(r)/pI:17.2 kDa,/ < 4.4; SSP 0114:M(r)/pI:17.6 kDa/ < 4.4) occur only in all LV gels but not in the RA gels. These five qualitatively differing spots are identical in DCM patients and in the healthy donor heart. Some of the differing spots were internally sequenced and identified as myosin light chain isoforms (myosin light chain 2, atrial; myosin light chain 2, ventricular; myosin light chain 1, atrial) with the Protein Identification Resource (PIR) accession numbers A44451, S03708, A30881, respectively. Additionally, phosphoglycerate mutase (PIR: JQ0750) and ATP synthase alpha chain (PIR: S17193) were identified. Thus, quantitative and qualitative differences between atrial and ventricular protein patterns were identified by 2-D PAGE. A characteristic distribution of myosin light chains between atrial and ventricular human myocardium was found using our approach.

Identification of proteins in polyacrylamide gels by mass spectrometric peptide mapping combined with database search

Mass spectrometric peptide mapping of proteins separated by one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis has been investigated. The best results are obtained after blotting of the proteins onto polyvinylidene difluoride membranes followed by enzymatic digestion of the protein on the membrane. The peptide maps were investigated in terms of completeness and applicability for protein identification using a previously developed database search program as well as for the possibility for full characterization of covalent modifications in the proteins. The most complete peptide maps were obtained when the proteins were reduced and alkylated on the membrane prior to enzymatic digestion followed by separation of the resulting mixture by high performance liquid chromatography prior to mass spectrometric analysis. Such peptide maps cover up to 98% of the sequence and consequently may allow complete characterization of post-translational modifications in proteins for which the amino acid sequence is known. The fastest and most sensitive procedure to obtain peptide maps sufficient for protein identification was direct analysis of the extracted peptide mixture by matrix-assisted laser desorption ionization (MALDI) mass spectrometry. The use of external and internal calibration of MALDI spectra for database searches is evaluated as well as the possibility of including a post-calibration routine within the search program.

Protein composition of the human heart: the construction of a myocardial two-dimensional electrophoresis database

Molecular changes occurring in myocardial diseases are not well understood. Proteins, as regulatory molecules, should play an important role in the etiology of these diseases. The method of two-dimensional electrophoresis (2-DE) allows the analysis of some thousand proteins with one experiment. An important prerequisite for this kind of investigation is the possibility of identifying the proteins separated by 2-DE. We resolve 3239 proteins of the human myocardium and tried to identify 33 proteins by amino acid analysis and microsequencing. Twenty proteins were identified by search for the protein-chemical data obtained in the Martinsried Institute Protein Sequence Database. Comparisons of 2-DE patterns of different size, which were obtained in different laboratories, were performed with the result that proteins identified on a 2-DE map of one laboratory can be assigned to spots of 2-DE maps produced by another laboratory. Our results show the usefulness of a myocardial 2-DE database; they can be used in different laboratories and make it possible to generate a collection of important human myocardial proteins in a 2-DE database for comparative studies worldwide.

Discovery and characterization of two novel human cancer-related proteins using two-dimensional gel electrophoresis

Comparative examination of protein synthesis in normal and neoplastic human fibroblasts led to the discovery of two novel microfilament proteins with roles in human neoplasia. One protein, a mutant beta-actin was found to convert nontumorigenic human fibroblasts to tumorigenicity. Recently, the oncogenic potential of this mutant beta-actin was verified independently and shown to alter the metastatic phenotype of human cells in conjunction with the myc and ras oncogenes. A second protein, leukocyte plastin, was discovered to be a marker of a majority of human cancer cells of nonhemopoietic origin. A survey of SV40-transformed human fibroblasts and human sarcoma and carcinoma cell types demonstrated that the L-plastin gene was activated at widely varying degrees in nearly all human cancer cells. Activation of the L-plastin gene was not detected in normal nonhemopoietic cells using sensitive reverse transcript-polymerase chain reaction, excepting those cells that expressed estrogen and progesterone receptors which mediate activation of L-plastin synthesis in reproductive tissues. Our most recent findings have revealed that activation of L-plastin synthesis in neoplastic cells that cannot phosphorylate L-plastin (e.g. those neoplastic cell types that express only trace amounts of L-plastin) results in the coinduction of two alternative inflammatory programs of gene expression which mediate cytolytic effects on surrounding cells. This inflammatory response appears to be mediated by "inappropriate" constitutive synthesis of L-plastin and failure of the induced cell to phosphorylate L-plastin. Our findings suggest explanations for the novel resistance of human cells to in vitro transformation and one role of oncogene activation in cancer. As a consequence of the interplay of two-dimensional (2-D) gel electrophoretic analyses with other sophisticated techniques of molecular biology, the formal characterization of two fundamentally important multigene families was completed with determination of many aspects of the structure and function of these proteins and their genes. The discovery and characterization of the mutant beta-actin and L-plastin and their relationship to the human neoplastic phenotype serve as useful models for the discovery of other important disease-related proteins/genes using 2-D gel electrophoresis.

The human keratinocyte two-dimensional gel protein database: update 1993

The master two-dimensional gel database of human keratinocytes currently lists 3038 cellular proteins (2127 isoelectric focusing, IEF; and 911 nonequilibrium pH gradient electrophoresis, NEPHGE) many of which correspond to post-translational modifications. 763 proteins have been identified (protein name, organelle components, etc.) and they are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Furthermore we have listed 176 proteins that have been microsequenced so far and that are recorded in this database. We also include synthetic images depicting some interesting sets of proteins identified so far; these include components of hnRNP's, proteasomes or prosomes, ribosomes, as well as assorted organelle markers, GTP-binding proteins, calcium binding proteins, stress proteins, autoantigens, differentiation markers and psoriasis upregulated proteins. The aim of the comprehensive database is to gather, through a systematic study of keratinocytes, qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and ultimately to pinpoint signaling pathways and components affected in various skin diseases, cancer included.

Protein ladder sequencing

A new approach to protein sequencing is described. It consists of two steps: (i) ladder-generating chemistry, the controlled generation from a polypeptide chain by wet chemistry of a family of sequence-defining peptide fragments, each differing from the next by one amino acid; and (ii) data readout, a one-step readout of the resulting protein sequencing ladder by matrix-assisted laser-desorption mass spectrometry. Each amino acid was identified from the mass difference between successive peaks, and the position in the data set defined the sequence of the original peptide chain. This method was used to directly locate a phosphoserine residue in a phosphopeptide. The protein ladder sequencing method lends itself to very high sample throughput at very low per cycle cost.

Analytical and micropreparative peptide mapping by high performance liquid chromatography/electrospray mass spectrometry of proteins purified by gel electrophoresis

We report the use of microbore reverse-phase high performance liquid chromatography connected on-line to an electrospray mass spectrometer for the separation/detection of peptides derived by proteolytic digestion of proteins separated by polyacrylamide gel electrophoresis. A small fraction (typically 10% of the total) of the peptides eluting from the column was diverted through a flow-splitting device into the ion source of the mass spectrometer, whereas the majority of the peptide samples was collected for further analyses. We demonstrate the feasibility of obtaining reproducible peptide maps from submicrogram amounts of protein applied to the gel and good correlation of the signal detected by the mass spectrometer with peptide detection by UV absorbance. Furthermore, independently verifiable peptide masses were determined from subpicomole amounts of peptides directed into the mass spectrometer. The method was used to analyze the 265-kDa and the 280-kDa isoforms of the enzyme acetyl-CoA carboxylase isolated from rat liver. The results provide compelling evidence that the two enzyme isoforms are translation products of different genes and suggest that these approaches may be of general utility in the definitive comparison of protein isoforms. We furthermore illustrate that knowledge of peptide masses as determined by this technique provides a major advantage for error-free data interpretation in chemical high-sensitivity peptide sequence analysis.

Mass spectrometric and Edman sequencing of lipocortin I isolated by two-dimensional SDS/PAGE of human melanoma lysates

We have integrated preparative two-dimensional polyacrylamide gel electrophoresis with high-performance tandem mass spectrometry and Edman degradation. By using this approach, we have isolated and identified, by partial sequencing, a human melanoma protein (34 kDa, pI 6.4) as lipocortin I. To our knowledge, this protein was not previously known to be associated with melanoma cells. The identity of the protein was confirmed by two-dimensional immunoblot analysis. High-energy collision-induced dissociation analysis revealed the sequence and acetylation of the N-terminal tryptic peptide and an acrylamide-modified cysteine in another tryptic peptide. Thus, knowledge concerning both the primary structure and covalent modifications of proteins isolated from two-dimensional gels can be obtained directly by this approach, which is applicable to a broad range of biological problems.

Human cellular protein patterns and their link to genome DNA mapping and sequencing data: towards an integrated approach to the study of gene expression

Analysis of cellular protein patterns by computer-aided two-dimensional gel electrophoresis together with recent advances in protein sequence analysis and expression systems have made possible the establishment of comprehensive two-dimensional gel protein databases that may link protein and DNA mapping and sequence information and that offer an integrated approach to the study of gene expression. With the integrated approach offered by two-dimensional gel protein databases it is now possible to reveal phenotype-specific protein(s), to microsequence them, to search for homology with previous identified proteins, to clone the cDNAs, to assign partial protein sequences to genes for which the full DNA sequence and the chromosome location are known, and to study the regulatory properties and function of groups of proteins that are coordinately expressed in a given biological process. Comprehensive two-dimensional gel protein databases will provide an integrated picture of the expression levels and properties of the thousands of protein components of organelles, pathways, and cytoskeletal systems, both under physiological and abnormal conditions, and are expected to lead to the identification of new regulatory networks. So far, about 20% (600 out of 2,980) of the total number of proteins recorded in the human keratinocyte protein database have been identified and we are actively gathering qualitative and quantitative biological data on all resolved proteins. Given the current improvements on microsequencing as well as the availability of specific antibodies, it seems feasible to expect that most known keratinocyte proteins will be identified in the very near future. This feast will reveal a wealth of new proteins that will become amenable to experimentation both at the biochemical and molecular biology level.

Identification of tissue proteins by amino acid analysis after purification by two-dimensional electrophoresis

Mouse brain proteins were separated by two-dimensional electrophoresis (2-DE). The proteins of a section of the 2-DE pattern were blotted onto hydrophobic membranes and 43 of them were excised and hydrolyzed by liquid-phase hydrolysis. The amino acid composition of these proteins was determined by orthophthaldialdehyde precolumn derivatization and compared with the compositions of known proteins stored in the NBRF sequence database. An identification program named ASA was developed for this purpose. The ASA program includes correction and weighting factors, data reduction by molecular weight windows, and exclusion or inclusion of certain organisms as desired. As a control, eight test proteins and five well-known proteins from mouse brain, all separated by 2-DE, were correctly identified by the program. Out of the 43 brain proteins selected, 19 were identified with high confidence.

Characterization of the periplasmic flagellum proteins of Leptospira interrogans

The structure and composition of periplasmic flagella (PF) from Leptospira interrogans serovar pomona type kennewicki were characterized. Electron microscopic observations showed that leptospiral PF were complex structures composed of an 11.3-nm-diameter core surrounded by two sheath layers with 21.5- and 42-nm diameters. Two-dimensional gel electrophoresis of isolated PF showed the presence of seven different proteins ranging in mass from 31.5 to 36 kDa. Rabbit polyclonal and mouse monoclonal antibodies against PF proteins were prepared and were used to localize specific proteins to portions of the PF structure by immunoelectron microscopy. A 34-kDa protein was associated with the 11.3-nm-diameter core filament, while a 36-kDa protein was associated with a PF sheath (21.5-nm-diameter filament). The amino termini of the 34- and 35.5-kDa proteins were homologous to PF core proteins of other spirochetes. The experimental data suggested that L. interrogans PF contains 2 proteins (34 and 35.5 kDa) in the PF core.